Proteins-DNA interaction on DNA cis-regulatory elements and further cross-talk among protein-DNA complexes decide precise transcription regulation. Since genes are embedded in huge DNA molecules, i.e., chromosomes of higher eukaryotes, which contain abundant of putative cis-regulatory elements such as enhancer and promoter sequences, this interaction of cis-regulatory sequences required for precise regulation of gene expression is extremely complicated. In order to achieve proper transcription regulation, selection of these interactions will be inevitable. Some of the DNA regions are believed to have roles for such traffic controls for these interactions among cis-regulatory elements.
Boundary elements divide a chromosome into units which are independent each other for transcription regulation. Several candidates for boundary elements were isolated mainly from genetic study of Drosophila melanogaster (M. Peifer and W. Bender, EMBO J. 1986, 5: 2293-2303; H. Gyurkovics et al., EMBO J. 1990, 9: 2579-2585; R. Kellum and P. Schedl, Mol. Cell. Biol. 1992, 12: 2424-2431; Georgiev and Corces, Proc. Natl. Acad. Sci. U.S.A., 1995, 92: 5184-5188; S. Barges et al., Development 2000, 127:779-790). Many of them are involved in the cis-regulatory elements for homeotic gene regulation (M. Peifer and W. Bender, EMBO J. 1986, 5: 2293-2303; H. Gyurkovics et al., EMBO J. 1990, 9: 2579-2585; S. Barges et al., Development 2000, 127:779-790). Use of an enhancer must be well organized to achieve proper transcription regulation of clustered homeotic genes to construct proper anterior-posterior segmental identity within an animal body. Mutations in these sequences give alterations in expression profiles of the genes and morphological shift of segmental identities (H. Gyurkovics et al., EMBO J. 1990, 9: 2579-2585; J. Mihaly et al., Development 1997, 124: 1809-1820).
Similar phenomenon has been observed also in mammalian orthologous homeotic genes (T. Kondo et al., Mol. Cell. 1998, 1: 289-300; M. Kmita et al., Nat. Genet. 2000, 26: 451-454). Homeobox Hox genes are responsible for anterior-posterior identity of the mammalian body as shown in Drosophila. Mis-regulation of Hox genes causes morphological alterations (T. Akasaka et al., Development 1996, 122: 1513-1522; N. Core et al., Development 2000, 124: 721-729) and can even be detrimental in some cases (T. Kondo and D. Duboule, Cell 1999, 97: 407-417; M. Kmita et al., Development 2002, 129: 5521-5528). As in the case of fruit fly, the enhancer-promoter interactions need to be organized for the Hox gene expression regulation (T. Kondo et al., Mol. Cell. 1998, 1: 289-300; M. Kmita et al., Nat. Genet. 2000, 26: 451-454). An enhancer that regulates the expression of Hoxd11 gene in cecum cannot associate to the promoter of Hoxd13 which is about 10 kb of distance from Hoxd11, whereas in mice with Hoxd12-Hoxd13 intergenic deletion the Hoxd13 gene gives its expression in cecum resembling Hoxd11 (T. Kondo et al., Mol. Cell. 1998, 1: 289-300; M. Kmita et al., Nat. Genet. 2000, 26: 451-454). Thus, it was concluded that Hoxd12-Hoxd13 intergenic sequence functions as an insulator.
Since the boundary element is expected to divide a chromosome into multiple units, enhancer activity cannot reach the promoter beyond the boundary sequence (which is called insulator activity). However, the enhancer insulation activity is only one aspect of boundary element. Addition to this, a boundary element also prevents the spreading of the heterochromatin which represses the expression of genes (J. Mihaly et al., Development 1997, 124: 1809-1820). Recently it is found that these two activities, insulation activity and position effect protection activity, can be separable from each other (F. Recillas-Targa et al., Proc. Natl. Acad. Sci. U.S.A., 2002, 99: 6883-6888).